title: O. sativa -Fe rep1

city: Porto Alegre

first: Andriele

last: Wairich

state: Rio Grande do Sul

address: Av. Bento Gonçalves, 9500

department: Center for Biotechnology

institute: Universidade Federal do Rio Grande do Sul

description:
lib_sativa_fe1
Pooled root tissues of Oryza sativa plants at the three leaf stage, cultivated under -Fe conditions

data_processing:
After sequencing, read quality was checked by FastQC, and all low quality reads (PHRED value < 30) were removed.
Adapter sequences were trimmed using Trim Galoreand the first twelve nucleotides were removed from the 5’ end.
The abundance of each transcript was estimated using Kallisto, and transcripts were considered differentially expressed when the False Discovery Rate (FDR) < 0.05.
Differentially expressed transcript annotations were downloaded from Ensembl plants database using the R package biomaRt.
Genome_build: O. sativa IRGSP-1.0 and O. rufipogon OR_W1943
Supplementary_files_format_and_content: format: tsv; 1st column: target ID; 2nd column: transcript lenght; 3rd column: effective lenght; 4rd column: estimated counts; 5rd column: transcripts per million (tpm)

organism: Oryza sativa

source_name: O. sativa -Fe_roots

growth_protocol: Rice seeds were germinated for four days in Petri dishes with filter paper soaked in distilled water at 28ºC (two days in the dark and two days in the light - 40 µmol.m-2.s-1). After germination, plants were transferred to vermiculite and cultivated for fifteen days. Then, plants were transferred to plastic pots with 0.5 L of nutrient solution containing 700 μM K2SO4, 100 μM KCl, 100 μM KH2PO4, 2 mM Ca(NO3)2, 500 μM MgSO4, 10 μM H3BO3, 0.5 μM MnSO4, 0.5 μM ZnSO4, 0.2 μM CuSO4, 0.01 μM (NH4)6Mo7O24, and 100 μM Fe+3-EDTA. After seven days, plants were transferred to control condition (CC) containing 100 μM Fe+3-EDTA) or to the Fe deficiency treatment (-Fe) for five days.

extract_protocol:
Total RNA was extracted using the Concert Plant RNA Reagent (Invitrogen®, Carlsbad, CA, USA), according to the manufacturer's instructions, quantified by Nanodrop and treated with DNAse I, Amplification Grade (Invitrogen®, Carlsbad, USA).
Approximately 20 µg of total RNA was used to high-throughput cDNA sequencing by Illumina HiSeq 2000 technology (Fasteris SA, Chemin du Pont-du-Centenaire, Switzerland – http://www.fasteris.com/). The cDNA libraries were prepared according to Illumina’s protocols.

treatment_protocol: Control Condition: 100 μM Fe+3-EDTA, Fe deficiency: no iron added to nutrient solution

tag: cultivar

value: O. sativa cv Nipponbare

tag: developmental stage

value: three leaf stage

value: roots

value: Fe deficiency


title: O. sativa -Fe rep2

status: Public on Nov 19 2019

type: SRA

country: Brazil

description:
lib_sativa_fe2
Pooled root tissues of Oryza sativa plants at the three leaf stage, cultivated under -Fe conditions

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: treatment


title: ATACseq_P6_4HPR_CB2

city: Toronto

first: Stephanie

middle: Zhi-Juan

last: Xie

state: ON

address: 101 College St. TMDT 8-401

country: Canada

institute: University Health Network

description: Cord blood 2

library_source: genomic

data_processing:
Each sample was aligned against hg19 using BWA with default parameters. All reads mapping to hg19 blacklist regions, mitochondrial genome, chrY or non-autosomal regions were removed. All reads with a quality score < 30 were removed.
MACS2 was used to identify significantly enriched regions of chromatin in each sample using default parameters plus the -llocal and -SPMR parameters.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak File

molecule: genomic DNA

organism: Homo sapiens

source_name: lineage depleted human cord blood cells

growth_protocol: Lin- CB at the 16 LTRC dose (62,500 cells/well, 24 well plate) were cultured with StemPro (Stem Cell Technologies) supplemented with StemPro nutrients (Stem Cell Technologies), L-glutamine (GIBCO), Pen/Strep (GIBCO), human LDL (Stem Cell Technologies, 50 ng/mL) and the following cytokines (all from Miltenyi): SCF (100 ng/mL), Flt3L (20 ng/mL), TPO (100 ng/mL), EPO (3 units/mL), IL-6 (50 ng/mL), IL-3 (10 ng/mL), GM-CSF (20 ng/mL) for 8 days.

extract_protocol:
Library preparation for ATAC-Sec was performed on 30,000 cells with Nextera DNA Sample Preparation kit (FC-121-1030, Iillumina), according to previously reported protocol (Buenrostro et al. 2013).
Libraries for ATAC were sequenced with HiSeq 2500 System (Illumina) to generate single-end 50-bp reads.

treatment_protocol: Cells were untreated, or DMSO, 2μM 4HPR, 35nM UM171 + 500 nM SR1 (U+S) or combination of 4HPR+UM171+SR1 (3-Factor) were added to cells and media at day 0. We mimicked fed-batch growth conditions where drug was added with fresh media every second day  for 8 days to reduce auto-inhibitory signalling and ensure nutrients and drugs are not limiting during the culture period (Csaszar et al., 2012): fresh media plus drugs are added on day 2 (0.5mls), day 4 (1ml), and feeding and transferring to a 6 well plate on day 6 (2 mls). Following ex vivo culture for 8 days, 4 pools of expanded lin-CB cells in the presence of indicated compounds were collected and subjected to CD34 enrichment with the CD34 Microbead kit (Miltenyi) on LS columns (Miltenyi). CD34+ enriched cells were then stained with CD45RA-FITC, CD90-PE, CD34 APC-cy7, and propidium iodide (PI) and 30,000 cLT (CD34+CD90+CD45RA-PI-) and cST (CD34+CD90-CD45RA-PI-) were sorted on the FACSAria Fusion (BD).

tag: pool

value: cord blood

tag: immunophenotypic cell population

value: cLT

tag: small molecule treatment


title: Day 1 Control rep 2

type: RNA

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

country: USA

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays 4X44K v2 (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or not significantly above background were excluded.

organism: Mus musculus

source_name: whole blood_Day 1 Control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were housed under standard vivarium conditions, and all procedures were conducted under an approved IACUC protocol.

extract_protocol: Mice were euthanized at 1, 2, 3, 5 or 7 days after irradiation. Blood was obtained via cardiac puncture and immediately added to a tube containing PAXgene Blood RNA stabilization and lysis solution at a ratio of 1:5 (blood:solution) and mixed. RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment, followed by globin reduction using GLOBINclear-Mouse/Rat.

treatment_protocol: Mice at 8-10 weeks of age were exposed in the early afternoon to total body radiation doses of 0, 1.5, 3, 6, or 10 Gy using an AECL Gammacell-40 137Cs gamma-ray source at a dose rate 1.05 Gy/ min.

tag: strain

tag: Sex

value: male

tag: age

value: 8-10 weeks

value: Day 1 Control

value: whole blood


title: Day 1 Control rep 4


title: ATACseq_P6_Combo_CB3

description: Cord blood 4


title: O. sativa CC rep2

description:
lib_sativa_cc2
Pooled root tissues of Oryza sativa plants at the three leaf stage, cultivated under control conditions

source_name: O. sativa CC_roots

value: Control


title: O. sativa CC rep1

description:
lib_sativa_cc1
Pooled root tissues of Oryza sativa plants at the three leaf stage, cultivated under control conditions


title: Day 1 Control rep 3


title: ATACseq_P7_DMSO_CB2

description: Cord blood 2

value: cST

value: DMSO


title: ATACseq_P6_DMSO_CB2

description: Cord blood 2


title: O. rufipogon -Fe rep2

description:
lib_rufipogon_fe2
Pooled root tissues of Oryza rufipogon plants at the three leaf stage, cultivated under -Fe conditions

organism: Oryza rufipogon

source_name: O. rufipogon -Fe_roots

value: O. rufipogon (BRA 00004909-8 accession from EMBRAPA Rice & Beans)


title: Day 1_1.5 Gy rep 3

source_name: whole blood_Day 1_1.5 Gy

value: Day 1_1.5 Gy


title: ATACseq_P6_None_CB2

description: Cord blood 2

value: untreated


title: ATACseq_P7_None_CB2

description: Cord blood 2


title: O. rufipogon CC rep2

description:
lib_rufipogon_cc2
Pooled root tissues of Oryza rufipogon plants at the three leaf stage, cultivated under control conditions

source_name: O. rufipogon CC_roots


title: O. rufipogon CC rep1

description:
lib_rufipogon_cc1
Pooled root tissues of Oryza rufipogon plants at the three leaf stage, cultivated under control conditions


title: ATACseq_P7_Combo_CB1

description: Cord blood 1


title: Day 1_1.5 Gy rep 2


title: Day 1_1.5 Gy rep 1


title: HBEC_RSV

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

data_processing:
Reads were de-multiplexed with the Illumina pipeline. Raw reads were aligned to a reference FASTA file that contains a curated list of transcripts (RefSeq, transcripts as of 2013). Alignment was done with BWA (Burrows-Wheeler Aligner) and reads per million (RPM) values were created from the sequence alignment map (SAM) output file
Messenger RNAs less than 200 bp were eliminated from the analysis.
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "mouse_refgu_ERCC.seq"
Supplementary_files_format_and_content: text file containing normalized (reads per million=RPM) expression values for genes 200 base pairs and longer

source_name: HBEC

growth_protocol: Airway epithelial cells were seeded in 24 well plates as follows: NCI-H292, passage 20, 250,000 cells/well;  A549, passage 12, 200,000 cells/well; human bronchial epithelial cells (HBECs), passage 4, 200,000 cells/well; small airway epithelial cells (SAECs), passage 4, 200,000 cells/well.  NCI-H292 and A549 cells were seeded in 500 ul RPMI + 1%FBS + 10 mM HEPES + 1 mM sodium pyruvate + pen/strep.  HBEC and SAEC cells were seeded in 500 ul BEBM + BEGM singlequots from Lonza or SABM + SAGM singlequots from Lonza, respectively.  The following day, compound dilutions were prepared in the same media with 0.2% DMSO and 250 ul with 2x compound was added to the approprate well.  For mock and viral infection, 250 ul of media alone or media containing RSV A2 MOI 1 was added to the appropriate wells for a total of 500 ul per well.  For ALI HBEC samples, HBECs that were cultured for 3 weeks at alir liquid interface (ALI) on transwell plates were infected with 10,000 or 50,000 pfu RSV.  Samples were collected at the indicated times by removing media, washing once with PBS and adding 300 ul RLT per well.

extract_protocol:
RNA was purified using RNeasy mini kits (Qiagen) according to the manufacturer’s protocol
one micrograms total RNA was used to make Illumina-compatible libraries using a custom protocol

tag: cell line

value: HBEC

value: epithelial

tag: infection

value: RSV


title: ATACseq_P7_US_CB1

description: Cord blood 1


title: ATACseq_P6_Combo_CB1

description: Cord blood 1


title: ATACseq_P6_US_CB1

description: Cord blood 1


title: H292_RSV_Dex

treatment_protocol: Airway epithelial cells were seeded in 24 well plates as follows: NCI-H292, passage 20, 250,000 cells/well;  A549, passage 12, 200,000 cells/well; human bronchial epithelial cells (HBECs), passage 4, 200,000 cells/well; small airway epithelial cells (SAECs), passage 4, 200,000 cells/well.  NCI-H292 and A549 cells were seeded in 500 ul RPMI + 1%FBS + 10 mM HEPES + 1 mM sodium pyruvate + pen/strep.  HBEC and SAEC cells were seeded in 500 ul BEBM + BEGM singlequots from Lonza or SABM + SAGM singlequots from Lonza, respectively.  The following day, compound dilutions were prepared in the same media with 0.2% DMSO and 250 ul with 2x compound was added to the approprate well.  For mock and viral infection, 250 ul of media alone or media containing RSV A2 MOI 1 was added to the appropriate wells for a total of 500 ul per well.  For ALI HBEC samples, HBECs that were cultured for 3 weeks at alir liquid interface (ALI) on transwell plates were infected with 10,000 or 50,000 pfu RSV.  Samples were collected at the indicated times by removing media, washing once with PBS and adding 300 ul RLT per well.

value: lung

value: Dexamethasone, 1 micromolar

tag: time point

value: 32 hours


title: H292_RSV


title: HBEC_mock

value: mock


title: ATACseq_P7_4HPR_CB1

description: Cord blood 1

value: cord blood


title: A549_RSV


title: H292_mock


title: ATACseq_P7_DMSO_CB1

description: Cord blood 1


title: A549_mock


title: ATACseq_P6_4HPR_CB1

description: Cord blood 1

value: cLT


title: Day 1 Control rep 1

value: male

value: 8-10 weeks

value: Day 1 Control


title: ATACseq_P6_DMSO_CB1

description: Cord blood 1


title: 32h_DMSO_mock

growth_protocol: NCI-H292 cells between passage 20 and 24 were seeded into 96 well plates at 70,000 cells/well in RPMI + 1%FBS + 10 mM HEPES + 1 mM sodium pyruvate + pen/strep.  The following day, compound dilutions were prepared in the same RPMI 1% FBS media with 0.2% DMSO and 50 ul was added to the approprate well.  For mock and viral infection, 50 ul of RMPI 1% FBS media or media containing 100,000 pfu RSV A2 GFP was added to the appropriate wells for a total of 100 ul per well.  For EGF treatment, 50 ul of 80 ng/ml EGF was added to the appropriate wells for a total of 100 ul per well of 40 ng/ml EGF.


title: O. rufipogon -Fe rep1

description:
lib_rufipogon_fe1
Pooled root tissues of Oryza rufipogon plants at the three leaf stage, cultivated under -Fe conditions

value: three leaf stage

value: roots

value: Fe deficiency


title: 32h_Dex_RSV

treatment_protocol: NCI-H292 cells between passage 20 and 24 were seeded into 96 well plates at 70,000 cells/well in RPMI + 1%FBS + 10 mM HEPES + 1 mM sodium pyruvate + pen/strep.  The following day, compound dilutions were prepared in the same RPMI 1% FBS media with 0.2% DMSO and 50 ul was added to the approprate well.  For mock and viral infection, 50 ul of RMPI 1% FBS media or media containing 100,000 pfu RSV A2 GFP was added to the appropriate wells for a total of 100 ul per well.  For EGF treatment, 50 ul of 80 ng/ml EGF was added to the appropriate wells for a total of 100 ul per well of 40 ng/ml EGF.


title: ATACseq_P6_None_CB1

description: Cord blood 1


title: iPS_RAG1_2

city: Parkville

first: Ali

last: Motazedian

state: Victoria

address: Royal Children's Hospital

department: Stem Cell Technology

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
10X single cell software (Cell Ranger) was used to preform secondary analysis including generation of Cell Ranger mkfastq and Cell Ranger count on each of the samples. This process produced filtered feature-barcode matrices MEX.
Genome_build: hg_38
Supplementary_files_format_and_content: The processed data files presented here are the output files generated via the cell ranger pipeline. The output “filtered_gene_bc_matrices” (only includes cellular barcodes) component was used for this study. This folder included 3 files; matrix.mtx file which contains the number of unique molecular identifiers (UMIs) associated with a gene (rows) and a cell (barcodes, columns), barcodes.tsv and genes.tsv files corresponding columns and rows of the mtx file, respectively.

source_name: human induced pluripotent stem cells

growth_protocol: Induced pluripotent stem cell lines were differentiated as embryoid bodies (EBs) for 8 days in presence of appropriate supplements. The EBs were then transferred onto Corning transmembranes to grow in air liquid interface system until the end of experiments.

extract_protocol:
iPSC derived RAG1:GFP+ purified cells were submitted to the Australian Genome Research Facility (AGRF) for single cell RNA sequencing using 10x Genomics Chromium system.
The sequencing and data generation was performed using AGRF- Illumina bcl2fastq pipeline version 2.20.0.422, via generation of 100bp Paired End reads and sequencing through Illumina HiSeq platform.

tag: experiment #

tag: differentiation day

tag: representative population

tag: sort parameters


title: 32h_DMSO_RSV

value: DMSO


title: 32h_Dex_mock


title: iPS_RAG1_1


title: HeLa.SMNDC1_poisonExon

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

description: RNA-seq of cell treated with the indicated pgRNA vector.

data_processing:
Illumina Casava software was used for base calling.
For RNA-seq, reads were aligned to the human transcriptome using RSEM followed by mapping to the human genome (hg19) using Bowtie and TopHat.
Gene expression estimates (TPM) were computed using RSEM and normalized using the TMM method.
Differentially expressed genes were defined as those passing specified Bayes factor (computed using Wagenmakers’s Bayesian framework) and fold-change threshold.
Genome_build: hg19
Supplementary_files_format_and_content: The final processed data is found in the file "d.expr.txt"

molecule: polyA RNA

extract_protocol:
For RNA-seq, all samples were collected into TRIzol and stored at -80°C until RNA was isolated. For pgRNA-seq, genomic DNA was extracted and stored at -20°C.
For RNA-seq, polyA-selected libraries were generated using the Illumina TruSeq kit.

treatment_protocol: pgRNAs vectors were designed to target ~500 ultraconserved "poison" exons. 9 pgRNAs were designed for each exon and 1,000 non-targeting controls were also included in the final library. We synthesized the pgRNA library with an oligonucleotide array and cloned the library at >1,000-fold coverage in order to maintain library diversity. All cloning followed procedures based on previous publications (PMID 27798563,28712454).

value: HeLa


title: HeLa.SMNDC1_upstreamExon


title: HeLa.SRSF3_upstreamExon


title: Tbk1 N129D1 WT MEF E1.5 treated with pI:pC - low cell density

city: Cambridge

first: Jea Hyun

last: Baek

state: Massachusetts

address: 225 Binney Street

institute: Biogen

data_processing:
Total reads were mapped using the aligner STAR
Genes were quantified with RSEM using OmicSoft Array Studio 10
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include COUNTS for each Sample

source_name: Murine embryonic fibroblast

growth_protocol: Murine embryonic fibroblasts were cultured in DMEM.

extract_protocol:
RNA was harvested using Qiagen RNeasy Plus Mini kit. Illumina TruSeq Stranded mRNA  Kit was used with 500 ng of total RNA for the construction of sequencing libraries.
RNAseq library were cleaned up with AMPure XP beads and QC checked with Caliper LabChip GX.

treatment_protocol: Cells were treated with pI:pC or antimycin/oligomycin for 4 h.

tag: cell type

value: Murine embryonic fibroblast

tag: genotype

value: wt/wt

value: pI:pC 4h


title: Tbk1 N129D1 WT MEF E1.5 - low cell density


title: HeLa.SNRNP70_upstreamExon


title: Tbk1 N129D1 WT MEF E1.5 treated with antimycin and oligomycin - low cell density

value: Antimycin + Oligomycin 4h


title: Tbk1 N129D1 WT MEF E1.5 treated with pI:pC - high cell density


title: Tbk1 N129D1 hom MEF E2.9 treated with antimycin and oligomycin


title: Tbk1 N129D1 WT MEF E1.5 treated with antimycin and oligomycin - high cell density


title: Tbk1 N129D1 WT MEF E1.5 - high cell density


title: PC9

description: RNA-seq of unperturbed cells.


title: HeLa.AAVS1


title: HeLa

description: RNA-seq of unperturbed cells.


title: Day2 10Gy rep3

source_name: whole blood_Day2 10Gy

value: Day2 10Gy

tag: tissue

value: whole blood


title: Tbk1 N129D1 hom MEF E1.4 treated with antimycin and oligomycin

tag: treatment


title: Tbk1 N129D1 hom MEF E2.9 treated with pI:pC


title: MPRA__DNA__rep1

city: Boston

first: Martha

middle: L.

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

description: plasmid DNA

data_processing:
Library strategy: MPRA
For MPRA samples, we used cutadapt to remove adapters from the raw reads and trim bases with a Phred score < 20. We then counted barcodes if they exactly matched an 11-bp barcode in the design index as well as the constant upstream 6 bp. All scripts used for subsequent data analysis of processed files can be found at https://github.com/kmattioli/2019__cis_trans_MPRA
For RNA-seq samples, we used Hisat2 to align reads hg19 or mm10. We used FeatureCounts to assign reads to genes in GENCODE v25 (lifted to hg19) and GENCODE vM13 (mm10).
Supplementary_files_format_and_content: Barcode counts and gene featureCounts.  The file index.txt.gz contains the chromosomal information for each barcode. This file is also available at: https://github.com/kmattioli/2019__cis_trans_MPRA/blob/master/data/01__design/02__index/index.txt.gz

organism: synthetic construct

source_name: plasmid DNA

growth_protocol: HUES64 cells were cultured in feeder-free mTeSR1 media and passaged every 5-7 days. mESC cells were cultured in feeder-free 2i media and passaged every 3-5 days.

extract_protocol:
RNA from transiently transfected cells was precipitated by phenol-chloroform extraction according to standard protocols. DNase treatment (Worthington) was followed by cDNA synthesis with SuperScript III First-Strand Synthesis System (Invitrogen).
cDNA was subject to library amplification and libraries were cleaned up with AMPure beads (0.6x, 1.6x, 1.0x).

treatment_protocol: Three different passaged of HUES64 cells were transiently transfected in triplicate (2.5 million cells each with 25 µg plasmid using 60 µL LipofectStem). Three different passages of mESC cells were transiently transfected (10 million cells each with 40 µg plasmid using 100 µL Lipofectamine 2000).

tag: experiment

value: MPRA


title: Tbk1 N129D1 hom MEF E2.2 treated with antimycin and oligomycin


title: ATACseq_P7_None_CB1

description: Cord blood 1

tag: pool

value: cord blood

tag: immunophenotypic cell population

value: cST

value: untreated


title: HIV_DRVTreat_4D S17

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were aligned to several human reference databases including hg19 human genome, exon, splicing-junction segments, and contamination database including ribosome and mitochondrial sequences using BWA alignment algorithm.
After filtering reads mapped to the contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 miss-matches for each transcript were then counted as expression level for the corresponding transcripts.
Supplementary_files_format_and_content: counts

source_name: Conditionally immortalized renal tubular epithelial cells (HPT1b)

growth_protocol: cells were expanded at 33c and then differentiated for 2 weeks to allow for T antigen degradation and differentiation before transduction

extract_protocol:
cells were scraped from plates and RNA isolated using
Sample QC analysis, cDNA library synthesis, and RNA sequencing were carried out by the Weill Cornell Genomics Core. The quality of RNA  was examined by Agilent bioanalyzer (Agilent). cDNA libraries were generated using TruSeq RNA Sample Preparation (Illumina). Each library was sequenced using single-reads in HiSeq4000 (Illumina).

tag: virus

value: VSV-pseudotyped gag/pol-deleted HIV

tag: drug treatment

value: darunavir 5uM x 4d (day 4-7 post transduction

tag: condition

value: HIV day 7, + darunavir

tag: batch


title: HIV_DRVTreat_4D S18


title: Tbk1 N129D1 hom MEF E2.2 treated with pI:pC


title: Tbk1 N129D1 hom MEF E2.9


title: Tbk1 N129D1 hom MEF E1.4 treated with pI:pC


title: CtrlV_DRVTreat_4D S12

value: VSV-pseudotyped EGFP lentivirus

value: EGFP control virus day 7, + darunavir


title: HIV_DRVTreat_4D S16


title: CtrlV_DRVTreat_4D S11


title: Tbk1 N129D1 hom MEF E2.2


title: HIV_NTreat_4D S15

value: HIV day 7, no drug


title: Tbk1 N129D1 het MEF E2.8 treated with antimycin and oligomycin


title: CtrlV_DRVTreat_4D S10


title: Tbk1 N129D1 het MEF E2.6 treated with antimycin and oligomycin


title: Tbk1 N129D1 het MEF E2.5 treated with antimycin and oligomycin


title: Tbk1 N129D1 hom MEF E1.4


title: HIV_NTreat_4D S14


title: HeLa.NTC

tag: cell line

value: HeLa


title: Tbk1 N129D1 het MEF E1.3 treated with antimycin and oligomycin

value: Murine embryonic fibroblast


title: Tbk1 N129D1 het MEF E2.8 treated with pI:pC


title: HIV_NTreat_4D S13


title: CtrlV_NTreat_4D S9

value: EGFP control virus day 7, no drug


title: CtrlV_NTreat_4D S8


title: Tbk1 N129D1 het MEF E2.6 treated with pI:pC

value: pI:pC 4h


title: CtrlV_NTreat_4D S7


title: Tbk1 N129D1 het MEF E1.3 treated with pI:pC


title: Tbk1 N129D1 het MEF E2.5 treated with pI:pC


title: Tbk1 N129D1 het MEF E2.6


title: Tbk1 N129D1 het MEF E2.8


title: Tbk1 N129D1 het MEF E1.3


title: HIV_NTreat S5

value: HIV day 4, no drug


title: HIV_NTreat S4


title: Tbk1 N129D1 het MEF E2.5


title: CtrlV_NTreat S2

value: EGFP control virus day 4, no drug


title: CtrlV_NTreat S3


title: CtrlV_NTreat S1


title: Tbk1 N129D1 WT MEF E2.7 treated with antimycin and oligomycin

value: wt/wt

value: Antimycin + Oligomycin 4h


title: HIV_NTreat S6


title: Tbk1 N129D1 WT MEF E2.1 treated with antimycin and oligomycin


title: Tbk1 N129D1 WT MEF E2.7 treated with pI:pC


title: 12hr_mock_infected.H5.batch3

city: Wurzburg

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Base calls were performed using the bulit in Illumina basecaller and demultiplexed using DeML
Sequenced reads were trimmed and quality checked using Trim Galore (v.0.4.3), FastQC (v.0.11.5) and FastQ-Screen (v.0.11.1)
Trimmed reads were aligned to the human genome (GRCh 38.87) using STAR (v.2.5.1a) keeping paired and unpaired aligned reads, genomic features were counted with FeatureCounts (v.1.5.0-p3)
Genome_build: Genome Reference Consortium Human Build 38 patch release 87 (GRCh38.p87)
Supplementary_files_format_and_content: Count matricies generated from each of the raw BAM files using FeatureCounts

source_name: Epithelial cells (HEp2)

growth_protocol: HEp-2 cells (American Type Culture Collection, ATCC No. CCL-23) were grown as monolayers in 6 x 100mm TC dishes until 90% confluent. Fresh monolayers were infected with Chlamydia trachomatis serovar E in 3.5 mL SPG buffer for an MOI ~ 1, using centrifugation  to synchronize infections. Infections and subsequent culture were performed in the absence of cycloheximide or DEAE dextran. A matching number of HEp-2 monolayers were also mock-infected using uninfected cell lysates. Each treatment was incubated at 25°C for  2h and subsequently washed twice with SPG to remove dead or non-viable EBs. 10 mL fresh medium (DMEM + 10% FBS, 25μg/ml gentamycin, 1.25μg/ml Fungizone) was added and cell monolayers incubated at 37°C with 5% CO2.

extract_protocol:
Single cell suspensions of time-matched mock-infected and Chlamydia trachomatis E-infected cells at 3, 6, and 12 hours post-infection were processed using the Fluidigm C1 scRNA-seq protocol according to the manufacturers instructions.
scRNA-Seq libraries were constructed using the standard protocol described for the Fluidigm C1 scRNA-seq.

treatment_protocol: Chlamydia trachomatis serovar E infections of HEp-2 cells and matched mock infections proceeded to 3, 6, and 12 hours post-infection before monolayer dissociation with trypsin.

value: epithelial (HEp2)

value: mock infected

tag: hours post infection

tag: sequencing batch

tag: chlamydial species


title: 12hr_mock_infected.G5.batch3


title: Tbk1 N129D1 WT MEF E1.5 treated with antimycin and oligomycin


title: Tbk1 N129D1 WT MEF E1.5 treated with pI:pC


title: Tbk1 N129D1 WT MEF E2.1 treated with pI:pC


title: 12hr_mock_infected.F6.batch3


title: Tbk1 N129D1 WT MEF E2.1


title: 12hr_mock_infected.D6.batch3


title: 12hr_mock_infected.E5.batch3


title: Tbk1 N129D1 WT MEF E2.7


title: 12hr_mock_infected.F5.batch3


title: Tbk1 N129D1 WT MEF E1.5


title: 12hr_mock_infected.E6.batch3


title: RNAseq_mESC_3_transfected_Rep1

description: genomic RNA

data_processing:
For MPRA samples, we used cutadapt to remove adapters from the raw reads and trim bases with a Phred score < 20. We then counted barcodes if they exactly matched an 11-bp barcode in the design index as well as the constant upstream 6 bp. All scripts used for subsequent data analysis of processed files can be found at https://github.com/kmattioli/2019__cis_trans_MPRA
For RNA-seq samples, we used Hisat2 to align reads hg19 or mm10. We used FeatureCounts to assign reads to genes in GENCODE v25 (lifted to hg19) and GENCODE vM13 (mm10).
Supplementary_files_format_and_content: Barcode counts and gene featureCounts.  The file index.txt.gz contains the chromosomal information for each barcode. This file is also available at: https://github.com/kmattioli/2019__cis_trans_MPRA/blob/master/data/01__design/02__index/index.txt.gz

source_name: mESC cell line

value: mESC cell line

value: RNA-seq


title: RNAseq_mESC_3_untransfected

description: genomic RNA


title: 12hr_mock_infected.D5.batch3


title: 12hr_mock_infected.C6.batch3


title: RNAseq_mESC_1_transfected_Rep1

description: genomic RNA


title: RNAseq_mESC_2_transfected_Rep1

description: genomic RNA


title: MPRA__mESC__rep3__tfxn1

description: GFP RNA

value: MPRA


title: 12hr_mock_infected.B5.batch3


title: RNAseq_mESC_1_untransfected

description: genomic RNA


title: 12hr_mock_infected.H6.batch3


title: 12hr_mock_infected.B6.batch3


title: 12hr_mock_infected.A6.batch3


title: 12hr_mock_infected.A5.batch3


title: 12hr_mock_infected.A1.batch3


title: 12hr_mock_infected.H4.batch2


title: 12hr_mock_infected.H3.batch2


title: MPRA__mESC__rep1__tfxn1

description: GFP RNA


title: MPRA__mESC__rep2__tfxn1

description: GFP RNA


title: RNAseq_mESC_2_untransfected

description: genomic RNA


title: 12hr_mock_infected.C5.batch3


title: 12hr_mock_infected.G4.batch2


title: 12hr_mock_infected.G3.batch2


title: 12hr_mock_infected.F4.batch2


title: 12hr_mock_infected.D3.batch2


title: 12hr_mock_infected.C3.batch2


title: 12hr_mock_infected.D4.batch2


title: 12hr_mock_infected.E3.batch2


title: RNA180129RH_1294_S30

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

data_processing:
FastQC was used for checking the quality of the raw sequence data.
Sequence data were then aligned using Spliced Transcripts Alignment to a Reference (STAR; Dobin et al., 2013), allowing for a maximum of 3 mismatches per 100 bp read with maximum number of multialigned reads = 1 (i.e, only uniquely aligned reads were used.
Reads were mapped to known genomic features to generate counts at the gene level using FeatureCounts (SubRead package).
Gene expression data were imported into R and an upper-quartile normalization was performed using edgeR (in R). Inclusion in the network analysis required a gene read density threshold of an average of greater than 1 count per million (CPM).
Network connectivity for coexpression was calculated
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: Raw counts in text format where each column provides read counts for each sample and each line provides the gene's EnsemblID

source_name: Dissected Tissue (Brain) - Ventrolateral Striatum

extract_protocol:
Animals were euthanized by cervical dislocation and brains were removed, flash frozen on dry ice, and kept at -80C until ventrolateral striatum was hand-dissected out. RNA was harvested using standard Trizol isolation, and Ovation RNA-Seq v2 kit was used to create amplified cDNA.
RNA libraries were prepared from cDNA for sequencing using Illumina TruSeq DNA library kit.
Samples were multiplexed six per lane on an Illumina HiSeq 2500 sequencer yielding 30-50 million single end reads(100 bp) per sample

treatment_protocol: Animals were all naïve, no treatment

tag: Sex

value: Male

tag: group

value: Low Drinker


title: RNA180129RH_1287_S27

value: Female


title: RNA180129RH_1252_S22


title: RNA180129RH_1262_S24


title: RNA180129RH_1292_S29

value: High Drinker


title: RNA180129RH_1247_S20


title: RNA180129RH_1254_S23


title: RNA180129RH_1223_S17


title: RNA180129RH_1291_S28


title: RNA180129RH_1278_S25


title: RNA180129RH_1248_S21


title: 12hr_mock_infected.E4.batch2

tag: cell type


title: RNA180129RH_1283_S26


title: 12hr_mock_infected.F3.batch2


title: 12hr_mock_infected.B4.batch2


title: 12hr_mock_infected.A4.batch2


title: 12hr_mock_infected.B3.batch2


title: RNA180129RH_1221_S15


title: RNA180129RH_1222_S16


title: 12hr_mock_infected.H9.batch1


title: 12hr_mock_infected.A3.batch2


title: 12hr_mock_infected.G9.batch1


title: 12hr_mock_infected.C4.batch2


title: RNA180129RH_1226_S19


title: RNA180129RH_1219_S13


title: 12hr_mock_infected.E9.batch1


title: 12hr_mock_infected.F9.batch1


title: RNA180129RH_1224_S18


title: 12hr_mock_infected.C9.batch1


title: RNA180129RH_1215_S11


title: RNA180129RH_1206_S8


title: 12hr_mock_infected.B9.batch1


title: 12hr_mock_infected.A9.batch1


title: 12hr_mock_infected.D9.batch1


title: RNA180129RH_1217_S12


title: 12hr_infected.H5.batch3

value: infected

value: Chlamydia trachomatis - Serovar E


title: 12hr_infected.G5.batch3


title: RNA180129RH_1205_S7


title: RNA180129RH_1199_S4


title: 12hr_infected.F5.batch3


title: 12hr_infected.F6.batch3


title: RNA180129RH_1200_S5


title: RNA180129RH_1202_S6


title: RNA180129RH_1198_S3


title: 12hr_infected.E5.batch3


title: RNA180129RH_1197_S2


title: RNA180129RH_1220_S14


title: RNA180129RH_1196_S1


title: 12hr_infected.E6.batch3


title: 12hr_infected.D6.batch3


title: RNA180129RH_1193_S47


title: RNA180129RH_1207_S9


title: RNA180129RH_1213_S10


title: RNA180129RH_1195_S48


title: 12hr_infected.H6.batch3


title: RNA180129RH_1192_S46


title: 12hr_infected.C6.batch3


title: 12hr_infected.D5.batch3


title: 12hr_infected.C5.batch3


title: 12hr_infected.B6.batch3


title: RNA180129RH_1189_S44


title: RNA180129RH_1185_S42


title: RNA180129RH_1188_S43


title: RNA180129RH_1191_S45


title: RNA180129RH_1184_S41


title: 12hr_infected.B5.batch3


title: 12hr_infected.A5.batch3


title: RNA180129RH_1183_S40


title: 12hr_infected.A6.batch3


title: RNA180129RH_1182_S39


title: 12hr_infected.H4.batch2


title: 12hr_infected.H3.batch2


title: 12hr_infected.G4.batch2


title: RNA180129RH_1180_S37


title: 12hr_infected.G3.batch2


title: 12hr_infected.F4.batch2


title: RNA180129RH_1176_S35


title: RNA180129RH_1179_S36


title: RNA180129RH_1175_S34


title: RNA180129RH_1170_S32


title: 12hr_infected.F3.batch2


title: 12hr_infected.E3.batch2


title: 12hr_infected.E4.batch2


title: RNA180129RH_1167_S31


title: 12hr_infected.D4.batch2


title: RNA180129RH_1162_S29


title: 12hr_infected.D3.batch2


title: 12hr_infected.C3.batch2


title: RNA180129RH_1171_S33


title: 12hr_infected.A1.batch3


title: RNA180129RH_1148_S27


title: 12hr_infected.B4.batch2


title: RNA180129RH_1146_S25


title: RNA180129RH_1166_S30


title: 12hr_infected.A4.batch2


title: RNA180129RH_1137_S24


title: RNA180129RH_1136_S23


title: RNA180129RH_1181_S38


title: 12hr_infected.H9.batch1


title: 12hr_infected.B3.batch2


title: RNA180129RH_1135_S22


title: RNA180129RH_1128_S21


title: 12hr_infected.G9.batch1


title: 12hr_infected.H10.batch1


title: 12hr_infected.G10.batch1


title: RNA180129RH_1127_S20


title: 12hr_infected.E9.batch1


title: 12hr_infected.F10.batch1


title: 12hr_infected.C4.batch2


title: RNA180129RH_1126_S19


title: RNA180129RH_1157_S28


title: RNA180129RH_1121_S18


title: 12hr_infected.F9.batch1


title: 12hr_infected.E10.batch1


title: RNA180129RH_1115_S16


title: RNA180129RH_1114_S15


title: RNA180129RH_1147_S26


title: 12hr_infected.D9.batch1


title: 12hr_infected.A3.batch2


title: RNA180129RH_1120_S17


title: RNA180129RH_1112_S13


title: RNA180129RH_1113_S14


title: RNA180129RH_1111_S12


title: RNA180129RH_1102_S11


title: RNA180129RH_1098_S10


title: 12hr_infected.C10.batch1


title: 12hr_infected.A9.batch1


title: 12hr_infected.B10.batch1


title: 12hr_infected.B9.batch1


title: 12hr_infected.A10.batch1


title: RNA180129RH_1095_S8


title: 12hr_infected.C9.batch1


title: RNA180129RH_1094_S7


title: 6hr_mock_infected.H6.batch3


title: RNA180129RH_1092_S5


title: 6hr_mock_infected.H5.batch3


title: 6hr_mock_infected.G5.batch3


title: 12hr_infected.D10.batch1


title: 6hr_mock_infected.F6.batch3


title: RNA180129RH_1091_S4


title: RNA180129RH_1093_S6


title: RNA180129RH_1088_S2


title: 6hr_mock_infected.E6.batch3


title: 6hr_mock_infected.E5.batch3


title: RNA180129RH_1090_S3


title: RNA180129RH_1087_S1


title: 6hr_mock_infected.F5.batch3


title: 6hr_mock_infected.D6.batch3


title: RNA180129RH_1085_S41


title: RNA180129RH_1083_S40


title: RNA180129RH_1077_S39


title: 6hr_mock_infected.C6.batch3


title: 6hr_mock_infected.C5.batch3


title: RNA180129RH_1097_S9


title: 6hr_mock_infected.D5.batch3


title: RNA180129RH_1076_S38


title: RNA180129RH_1072_S37


title: 6hr_mock_infected.B6.batch3


title: 6hr_mock_infected.B5.batch3


title: RNA180129RH_1050_S36


title: 6hr_mock_infected.A6.batch3


title: UC-MSC rep3

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

country: Japan

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

data_processing:
The Illumina Hiseq generates raw images utilizing HCS (HiSeq Control Software v2.2) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4). Adapters are not trimmed away from the reads.
The 50-bp-long single-end sequence reads were mapped to a mouse genome reference sequence (mouse GRCm38/mm10) using CLC Genomics workbench (Qiagen), and the mapped data were imported into Strand NGS analysis software (Agilent Technologies, Santa Clara, CA, USA) and expression of RNA was quantified with Deseq normalization.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

source_name: colon obtained from mouse with DSS-induced colitis and injected with UC-MSC

extract_protocol:
The excised medial colons were stored frozen at -80°C. Total RNA was extracted from these samples using an RNeasy Mini kit (Qiagen N.V., Venlo, the Netherlands) according to the manufacturer’s instructions. Tissue disruption and cell lysis were performed in buffer RLT in a GentleMACS Dissociator (Miltenyi Biotec K.K., Tokyo, Japan) using the pre-set program (RNA_02) for total RNA extraction. Samples with an RNA integrity number of less than 7 were excluded from further processing and analysis.
Libraries for RNA-sequencing (RNA-seq) were constructed using a SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Takara Bio, Shiga, Japan) according to the manufacturer’s instructions.

tag: strain

value: colon

tag: age

value: 10 to 12 weeks old

value: male


title: UC-MSC rep1

tag: tissue


title: 6hr_mock_infected.A5.batch3


title: UC-MSC rep2


title: 6hr_mock_infected.A1.batch3


title: 6hr_mock_infected.H3.batch2


title: 6hr_mock_infected.H4.batch2


title: Control rep3

source_name: colon obtained from mouse with DSS-induced colitis and injected with PBS


title: AD-MSC rep1

source_name: colon obtained from mouse with DSS-induced colitis and injected with AD-MSC


title: AD-MSC rep2


title: AD-MSC rep3


title: Control rep2


title: Control rep1


title: 6hr_mock_infected.E3.batch2


title: 6hr_mock_infected.G4.batch2


title: 6hr_mock_infected.F3.batch2


title: 6hr_mock_infected.D4.batch2


title: 6hr_mock_infected.G3.batch2


title: 6hr_mock_infected.C3.batch2


title: 6hr_mock_infected.B4.batch2


title: 6hr_mock_infected.A4.batch2


title: 6hr_mock_infected.A3.batch2


title: 6hr_mock_infected.B3.batch2


title: 6hr_mock_infected.H9.batch1


title: 6hr_mock_infected.D3.batch2


title: 6hr_mock_infected.F9.batch1


title: 6hr_mock_infected.C4.batch2


title: 6hr_mock_infected.G10.batch1


title: 6hr_mock_infected.G9.batch1


title: 6hr_mock_infected.F10.batch1


title: 6hr_mock_infected.E4.batch2


title: 489-860: mouse_liver_LCA_3

city: Düsseldorf

first: Verena

last: Keitel

address: Moorenstr. 5

department: Department of Gastroenterology, Hepatology and Infectious Diseases

institute: University Hospital, Medical Faculty of Heinrich Heine University Düsseldorf

hyb_protocol: End-labelled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST Gene Expression Microarrays for 16 h at 45 °C, stained by strepatavidin/phycoerythrin conjugate

scan_protocol: Arrays were scanned as described in the manufacturers´ protocol.

data_processing: Normalization of the raw microarray data (CEL files) was done using RMA as implemented in the R package oligo. Normalization was performed on a set of in total 18 CEL files.

label: biotin

source_name: liver tissue of TGR5 wildtype mice

label_protocol: Synthesis of biotin-labelled cDNA was performed according to the manufacturers´ protocol (WT Plus Reagent Kit; Affymetrix, Inc). Briefly, 100 ng of total RNA were converted to cDNA. After amplification by in vitro transcription and 2nd cycle synthesis, cDNA was fragmented and biotin labelled by terminal transferase.

growth_protocol: Mice were bred and kept in the central animal facility of Duesseldorf University (ZETT) and had access to water and food ad libitum. A 12h light/dark cycle was maintained.

extract_protocol: RNA from liver samples of the mice or was extracted using the Maxwell 16 LEV simply RNA Tissue Kit (Promega, Madison, USA) and the Maxwell 16 Instrument (Promega, Madison, USA) according to the manufacturer’s instructions.

treatment_protocol: TGR5 WT male mice aged 8-12 weeks were fed a diet containing 1% (w/w) lithocholic acid (LCA, ssniff, Soest, Germany) for 84h or standard chow diet ad libitum.

tag: gender

tag: chow

value: LCA


title: 489-829: mouse_liver_LCA_2


title: 6hr_mock_infected.E9.batch1


title: 489-862: mouse_liver_LCA_5


title: 489-861: mouse_liver_LCA_4


title: 489-864: mouse_liver_LCA_6


title: 6hr_mock_infected.H10.batch1


title: 489-772: mouse_liver_LCA_1


title: 489-705: mouse_liver_control_4

value: control


title: 489-774: mouse_liver_control_3


title: 489-702: mouse_liver_control_2


title: 6hr_mock_infected.E10.batch1


title: 6hr_mock_infected.D9.batch1


title: mouse_spleen_nonvaccinated_infected_16wks_rep2

city: Philadelphia

first: Theresa

last: Busch

state: PA

address: 13400 Civic Center Blvd

department: Radiation Oncology

institute: University of Pennsylvania

hyb_protocol: Hybridization took place for 16 h in an Affymetrix GeneChip ® Hybridization Oven 640. Affymetrix GeneChip® Fluidics Station 450 was then used to wash and stain the arrays with streptavidin-phycoerythrin according to the standard antibody amplification protocol for eukaryotic targets.

scan_protocol: Arrays were scanned on Affymetrix GeneChip ® Scanner 3000 at 570 nm. Images were acquired using the Affymetrix ® GeneChip ® Command Console ® Software (AGCC).

data_processing: Primary analysis was performed using R/Bioconductor. rma() function from R package oligo was used for background correction, quantile normalization and log summarization of probe sets. Subsequent analyses were carried out after (i) keeping only probe sets that in more than half of the samples exhibited an intensity higher than the first quartile of the median intensities between samples and (ii) removing unannotated probe sets (Entrez IDs). Limma moderated t-tests and one-way ANOVA were used to identify genes that varied significantly between two or more than two groups respectively. Benjamini-Hochberg procedure was utilized to adjust for multiple comparisons.

source_name: spleen tissue, female 6-8 weeks old BALB/c mouse

label_protocol: Approximately 300 ng of total RNA were used to generate biotinylated complementary RNA (cRNA) for each group using the GeneChip ® WT PLUS Reagent Kit protocol for Whole Transcript (WT) Expression Array, Rev3. Poly-A RNA control added to the RNA test samples as exogenous positive control and the RNA was reverse-transcribed to double stranded cDNA and biotinylated cRNA was synthesized and purified according to the protocol. A 2nd cycle of cDNA synthesis followed along with a second purification step. Then, 6μg of the single-stranded DNA was fragmented, labeled with the appropriate labeling reagent and hybridized to GeneChip ® Mouse Gene 2.0 ST arrays (Affymetrix, Thermo Fisher Scientific).

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted from sampled spleen tissue that was aseptically excised, snap frozen in liquid nitrogen and stored at -80 ºC using RNeasy Microarray Tissue kit (Qiagen, Maryland, USA) following manufacturer’s instructions. RNA was checked for integrity using the RNA 6000 NanoLabChip kit on Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA). Only RNA samples with RIN > 7.0 were utilized for microarray analysis.

treatment_protocol: BALB/c mice were vaccinated thrice with two weeks intervals with CPA160-189-loaded p8-PLGA nanoparticles. Mice receiving PBS alone served as controls. Two weeks after each injection, mice were challenged with L. infantum promastigotes. Non-vaccinated non-infected (naive) mice served as negative control group. At 4 and 16 weeks post challenge spleens were aseptically extracted from individual mice and sample tissues were snap frozen in liquid nitrogen.

tag: challenge status

tag: vaccination status

value: non-vaccinated

tag: weeks post-challenge


title: 489-701: mouse_liver_control_1


title: 6hr_mock_infected.C10.batch1

value: epithelial (HEp2)

tag: condition


title: 6hr_mock_infected.C9.batch1

value: mock infected


title: Lonp1_IP

city: Worcester

first: pengpeng

last: liu

address: 436 Plantation St

department: MCCB

institute: umassmed

data_processing:
Basecalls performed using CASAVA version 1.8
he quality of the raw sequencing data was first evaluated with fastqc (0.11.5). ChIP-seq reads were aligned to the WBcel220(ce10) worm genome by using by Burrows-Wheeler Aligner (BWA MEM, BWA version 0.7.15) algorithm with the standard default settings.
The duplicated reads were removed using picard tools v1.96.
Peaks were determined using MACS version 2.135 with the no-model parameter.IgG was used as a control for peak-calling, and the bigwig files were generated with the signal as fold enrichment by macs2 following the procedure: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: WBcel220(ce10)
Supplementary_files_format_and_content: ChIP-seq bigwig files were generated using MCAS 2.135; Scores represent the ChIP-seq tag numbers,

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
Synchronized worms were cultured in liquid and harvested at early L4 stage by sucrose flotation.  The worms were lysed via Teflon homogenizer in cold PBS with protease inhibitors (Roche). Cross-linking of DNA and protein was performed by treating the worms with 1.85% formaldehyde for 15 min. Glycine was added to a final concentration of 125mM for 5 min at room temperature to quench the formaldehyde. The pellets were resuspended twice in cold PBS with protease inhibitor. Samples were sonicated in Bioruptor (Diagenode) for 15 min at 4°C on high intensity (30s on and 30s off). Samples were transferred to microfuge tubes and spun at 15,000*g for 15 min at 4°C. The supernatant was precleaned with pre-blocked ChIP-grade Pierce™ magnetic protein A/G (Thermo Scientific) and then incubated with Monoclonal ANTI-FLAG® M2 antibody (Sigma, F1804) or Mouse mAb IgG1 Isotype Control (Cell Signaling Technology, G3A1) rotating overnight at 4°C. Then, the antibody-chromatin complex was precipitated with magnetic beads or protein A sepharose beads (Invitrogen) dependent on the host of generated antibodies. After washing, the crosslinks were reversed by incubation at 65 °C overnight and further treated with RNaseA 37 °C for 1 hour and then proteinase K 55 °C for 2 hours, respectively.
Finally, immunoprecipitated and input DNA were purified with ChIP DNA Clean & Concentrator (Zymo Research, D5205) and used as templates for qPCR or next generation sequencing.

tag: strain background

tag: genotype/variation

tag: developmental stage

value: L4 stage hermaphrodite worms

tag: chip antibody

value: Monoclonal ANTI-FLAG M2 antibody (Sigma, F1804)


title: Lonp1_IgG

growth_protocol: Synchronized worms were cultured in liquid and harvested at early L4 stage by sucrose flotation.

treatment_protocol: The worms were lysed via Teflon homogenizer in cold PBS with protease inhibitors (Roche). Cross-linking of DNA and protein was performed by treating the worms with 1.85% formaldehyde for 15 min. Glycine was added to a final concentration of 125mM for 5 min at room temperature to quench the formaldehyde. The pellets were resuspended twice in cold PBS with protease inhibitor. Samples were sonicated in Bioruptor (Diagenode) for 15 min at 4°C on high intensity (30s on and 30s off). Samples were transferred to microfuge tubes and spun at 15,000*g for 15 min at 4°C. The supernatant was precleaned with pre-blocked ChIP-grade Pierce™ magnetic protein A/G (Thermo Scientific) and then incubated with Monoclonal ANTI-FLAG® M2 antibody (Sigma, F1804) or Mouse mAb IgG1 Isotype Control (Cell Signaling Technology, G3A1) rotating overnight at 4°C. Then, the antibody-chromatin complex was precipitated with magnetic beads or protein A sepharose beads (Invitrogen) dependent on the host of generated antibodies. After washing, the crosslinks were reversed by incubation at 65 °C overnight and further treated with RNaseA 37 °C for 1 hour and then proteinase K 55 °C for 2 hours, respectively. Finally, immunoprecipitated and input DNA were purified with ChIP DNA Clean & Concentrator (Zymo Research, D5205) and used as templates for qPCR or next generation sequencing.


title: mouse_spleen_vaccinated_infected_16wks_rep1

value: vaccinated


title: mouse_spleen_nonvaccinated_infected_16wks_rep1


title: 6hr_mock_infected.A9.batch1

tag: hours post infection

tag: sequencing batch

tag: chlamydial species


title: mouse_spleen_nonvaccinated_infected_4wks_rep1


title: 6hr_mock_infected.A10.batch1

tag: cell type


title: 6hr_mock_infected.B10.batch1


title: 6hr_infected.H6.batch3


title: mouse_spleen_vaccinated_infected_16wks_rep2


title: mouse_spleen_vaccinated_infected_4wks_rep2


title: mouse_spleen_naïve_rep1

value: uninfected

value: naïve


title: mouse_spleen_naïve_rep2


title: 6hr_infected.H5.batch3


title: 6hr_mock_infected.D10.batch1


title: mouse_spleen_vaccinated_infected_4wks_rep1


title: 6hr_infected.G5.batch3


title: 6hr_infected.F6.batch3


title: 6hr_infected.F5.batch3


title: 6hr_mock_infected.B9.batch1


title: 6hr_infected.E6.batch3


title: Muscle_24hr_rep1

city: Nagoya

first: Tetsuya

last: Horita

state: Aichi

address: 1 Kawasumi Mizuho-cho Mizuho-ward

department: Department of Forensic Medicine

institute: Nagoya City University Graduate School of Medical Sciences

description: Gene expression in biceps femoris muscle of mouse with incision 12 h after injury

hyb_protocol: SurePrint G3 Mouse Gene Expression Microarray Kit <G4852A> (Agilent) and Hybridization Gasket Slide Kit (5) -8 microarrays per slide format <G2534-60014> (Agilent) were used as analysis chips. Moreover, Gene Expression Hybridization Kit <5188-5242> (Agilent) was used as a reagent kit.  (1) A fragmentation reaction was performed for 600 ng for purified probe (60 ° C, 30 minutes). (2) The hybridization reagent was mixed, and 480 ng of probe was hybridized with the analysis chip (65 ° C., 17 hours, 10 rpm) by hybridization oven <G2545A，G2530-60029> (Agilent). (3) The work from Wash to the end of Scanning was done in the ozone booth using Gene Expression Buffer Kit <5188-5327> (Agilent). Wash Buffer 1 = RT, 1 min. Wash Buffer2 = 37° C, 1min. (4) After washing, the chip was dried (remaining water droplets were removed with nitrogen gas).

scan_protocol: Slides were scanned after washing on the Scanner <G2539A: (for samples of C and 12h), G2505C: (for samples of 6h and 24h)> (Agilent) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction <version 10.10.1.1> (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20130207 (for samples of C and 12h) or 028005_D_F_20150604: (for samples of 6h and 24h)). Based on the scanned image, raw data were obtained by subtracting the background value of the spot from the numerical value of the spot where each probe was hybridized.

source_name: biceps femoris muscle, incision, 24hr

label_protocol: (1): cDNA was prepared using poly dT primer with T7 promoter of Low Input Quick Amp labeling kit, one-color <5190-2305> (Agilent) and reverse transcriptase for 100 ng RNA (37 ° C, 2 hours). (2): RNA was synthesized from the prepared cDNA and T7 RNA polymerase. At this time, Cy dye (Cy3) was added to synthesize RNA labeled with Cy dye  using Agilent RNA Spike-In kit <5188-5282> (Agilent Technologies) (37 ° C, 2 hours). (3): To purified as a probe, Cy dye that was not labeled was removed by RNeasy mini kit <74106> (Qiagen). (4) Dye incorporation and cRNA yield were checked with the Nanodrop ND1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the muscle samples (control and 6, 12, 24 h post-injury groups; n = 4 for each group) with RNeasy Fibrous Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Samples were processed with RNase-free water and treated with DNase I stock solution for prevention of genomic contamination. RNA was quantified using a Nanodrop ND1000 <version 3.5.2> (Thermo Fisher Scientific, Waltham, MA) spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples of control and 6, 12, 24 h were outsourced to perform the microarray analysis (Oncomics Co. Ltd., Nagoya, Japan)

value: biceps femoris muscle

tag: strain

value: BALB/c

tag: incision

value: with incision

tag: time point

value: 24 h after injury


title: Muscle_24hr_rep3

tag: tissue

tag: gender


title: Muscle_12hr_rep4

source_name: biceps femoris muscle, incision, 12hr

value: 12 h after injury


title: Muscle_12hr_rep3


title: Muscle_24hr_rep4


title: 6hr_infected.E5.batch3

value: infected

value: Chlamydia trachomatis - Serovar E


title: 6hr_infected.C6.batch3


title: 6hr_infected.D5.batch3


title: 6hr_infected.C5.batch3


title: 6hr_infected.D6.batch3


title: 6hr_infected.B5.batch3


title: 6hr_infected.B6.batch3


title: D10 144.5 GFP+_3

city: Melbourne

first: Katrina

middle: M

last: Bell

address: RCH, Flemington Rd, Parkville

institute: MCRI

description:
miRNA
15_C5HG9ACXX_ATGTCA_L004_R1

data_processing:
HiSEQ 2000
CASAVA 1.8.2 pipeline was used to generate the sequence data
Fastqc was implemented to assess quailty of sequence. Adapter and primer sequences were removed using cutadapt. Bowtie aligner was used to map the 17-26 base pair single end reads to the human reference genome (hg19) allowing one mismatch.
The uniquely mapped reads were summarized across miRNA with featureCounts (Rsubread v1.20.6) using ensemble miRNA gene annotation. Lowly expressed miRNAs were filtered out (less than 10 counts per million in fewer than three samples).
The data was Voom transformed with cyclic loess normalization, and differential expression assessed using empirical Bayes moderated t-tests from the R Bioconductor limma(version 3.20.9) package
Genome_build: hg19
Supplementary_files_format_and_content: read count of features from featureCounts with miRNA ensemble gene annotation

source_name: human embryonic stem cells

growth_protocol: hESC single-cell suspension (0.8x106 cells/well) were resuspended in RPMI/B27 medium minus insulin, supplemented with 2mM L-glutamine, penicillin/streptomycin (referred to as monolayer differentiation media) containing 12µM CHIR99021, 80 ng mL-1 Activin A, 50µg mL-1Ascorbic Acid and seeded onto a Geltrex coated 12-well plate. After 24 hours (day 1 of differentiation), medium was aspirated and replaced with fresh monolayer differentiation medium supplemented with 5 µM IWR-1  and 50µg mL-1 Ascorbic Acid. On day 3 of differentiation, the IWR-1 and Ascorbic Acid monolayer differentiation medium was removed and the medium was subsequently refreshed every two days until day seven. Cells were then maintained in monolayer differentiation medium until harvested for analysis.

extract_protocol:
Differentiated cells were single cell sorted based on GFP expression via flow cytometry,flash frozen on dry ice, and miRNA was harvested using Qiagen miRNANeasy Mini kit  (Cat#217004). A minimum amount of 500ng of total small RNAs was used in the construction of sequencing libraries.
Small RNA libraries were prepared using TruSeq Small RNA Sample Prep Kit (Illumina)

tag: genotype

value: NKX2-5 null (NKX2-5eGFP/eGFP)

value: early cardiomyocyte


title: 6hr_infected.A6.batch3


title: 6hr_infected.A5.batch3


title: Muscle_24hr_rep2

value: male


title: D10 144.5 GFP+_2

description:
miRNA
14_C5HG9ACXX_AGTTCC_L004_R1


title: Muscle_12hr_rep1


title: Muscle_non_rep2

description: Gene expression in biceps femoris muscle of mouse without incision

source_name: biceps femoris muscle, no incision, 0hr

value: without incision


title: D10 144.5 GFP+_1

description:
miRNA
13_C5HG9ACXX_AGTCAA_L004_R1


title: D10 NKX.25 GFP+_3

description:
miRNA
12_C5HG9ACXX_CTTGTA_L004_R1

value: NKX2-5 het (NKX2-5eGFP/w)


title: 6hr_infected.A1.batch3

value: epithelial (HEp2)


title: Muscle_12hr_rep2


title: 6hr_infected.H4.batch2


title: Muscle_non_rep4


title: Muscle_6hr_rep4

description: Gene expression in biceps femoris muscle of mouse with incision 6 h after injury

source_name: biceps femoris muscle, incision, 6hr

value: 6 h after injury


title: Muscle_6hr_rep3


title: Muscle_non_rep3


title: Muscle_6hr_rep2


title: Muscle_non_rep1


title: Muscle_6hr_rep1


title: D10 NKX.25 GFP+_2

description:
miRNA
11_C5HG9ACXX_GGCTAC_L004_R1


title: 6hr_infected.H3.batch2


title: 6hr_mock_infected.F4.batch2

value: mock infected


title: D10 NKX.25 GFP+_1

description:
miRNA
10_C5HG9ACXX_TAGCTT_L004_R1


title: 3BMB_152

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

value: lung


title: D6 144.5 GFP+_3

description:
miRNA
9_C5HG9ACXX_GATCAG_L004_R1

value: cardiac progenitor


title: 6hr_infected.G3.batch2


title: 3BMB_65


title: 6hr_infected.G4.batch2


title: 3BMB_157


title: 3BMB_49


title: 3BMB_160


title: 3BMB_181


title: 3BMB_54


title: D6 144.5 GFP+_1

description:
miRNA
7_C5HG9ACXX_CAGATC_L004_R1


title: 3BMB_106


title: D6 NKX.25 GFP-_2

description:
miRNA
5_C5HG9ACXX_ACAGTG_L004_R1

value: pre-NKX2-5 mesoderm


title: 3BMB_72


title: D6 NKX.25 GFP-_3

description:
miRNA
6_C5HG9ACXX_GCCAAT_L004_R1


title: D6 144.5 GFP+_2

description:
miRNA
8_C5HG9ACXX_ACTTGA_L004_R1


title: 3BMB_99


title: 6hr_infected.E3.batch2


title: 6hr_infected.F3.batch2


title: 6hr_infected.F4.batch2


title: D6 NKX.25 GFP-_1

description:
miRNA
4_C5HG9ACXX_TGACCA_L004_R1


title: 6hr_infected.D4.batch2


title: D6 NKX.25 GFP+_3

description:
miRNA
3_C5HG9ACXX_TTAGGC_L004_R1


title: 6hr_infected.E4.batch2


title: 6hr_infected.D3.batch2


title: 3BMB_39


title: 3BMB_36


title: 6hr_infected.C4.batch2


title: 3BMB_153


title: Z36_3

city: Beijing

first: Bin

last: Xia

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

data_processing:
Illumina Bcl2fastq conversion software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for contamination sequences and low-quality sequences. Then counted reads and calculated GC-content.
After verifing the data quality, reads were mapped to hg19 whole genome using CWA version 0.5.9 with the default parameters in the software.
Reads Per Kilobases per Million mapped reads of library size (RPKM) were calculated using the equation by Ali Mortazavi et al. in 2008.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include RPKM values and reads per gene for each Sample.

extract_protocol:
HeLa cells were collected and resuspended with PBS into a 1.5-ml microfuge tube after treatments. Samples were centrifuged at 1000 rpm for 3 mins to pellet the cells at room temperature. Total RNAs were extracted with the RNeasy Mini kit (QIAGEN, Cat. No. 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HeLa cells treated with DMSO (as control), 1 μM Rapa or 13 μM Z36, in two biological replaecs, for 10 hours before RNA extraction.

tag: cell line

value: HeLa

tag: tissue source

value: cervix

tag: treatment


title: D6 NKX.25 GFP+_2

description:
miRNA
2_C5HG9ACXX_CGATGT_L004_R1


title: D6 NKX.25 GFP+_1

description:
miRNA
1_C5HG9ACXX_ATCACG_L004_R1


title: 3BMB_91


title: 6hr_infected.B4.batch2

tag: condition


title: 3BMB_86


title: 3BMB_177


title: 3BMB_38


title: 3BMB_44


title: Z36_1


title: 3BMB_166


title: 3BMB_88


title: 6hr_infected.B3.batch2


title: 3BMB_136


title: 3BMB_10


title: 3BMB_140


title: mouse_spleen_nonvaccinated_infected_4wks_rep2

tag: challenge status

tag: vaccination status

value: non-vaccinated

tag: weeks post-challenge


title: 3BMB_130


title: 3BMB_141


title: 3BMB_149


title: 6hr_infected.C3.batch2

tag: hours post infection


title: 3BMB_108


title: Rapa_3

value: Rapamycin


title: 6hr_infected.A4.batch2

value: infected

tag: sequencing batch


title: 3BMB_147


title: Rapa_1


title: NC_3

value: DMSO as control


title: 3BMB_100


title: 3BMB_137


title: 3BMB_69


title: 6hr_infected.H10.batch1

tag: chlamydial species

value: Chlamydia trachomatis - Serovar E


title: NC_1


title: 6hr_infected.G9.batch1

tag: cell type


title: 3BMB_122


title: 3BMB_125


title: 6hr_infected.G10.batch1


title: 3BMB_33


title: 6hr_infected.A3.batch2


title: 3BMB_143


title: 3BMB_148


title: 3BMB_5


title: 6hr_infected.F9.batch1


title: 6hr_infected.H9.batch1


title: 6hr_infected.E9.batch1


title: UIC - sorted uninfected cells from infected well

first: Effie

middle: Efthimia

last: Bastounis

address: UW Biology Life Sciences Bldg, Room 565, 4000 15th Ave NE

department: Biology

institute: University of Washington

description: 2x10^5 cells grown on 12 mm collagen I coated glass coverslips for 24 h were then exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria, media containing 20 μg/mL gentamycin was added to cells. 24 h post-infection cells were trypsinized, infected cells were  flow sorted and then RNA was extracted.

data_processing:
Raw sequencing data generated from Illumina NovaSeq 6000 that pass the Illumina chastity filter are used for following analysis. Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on alignment statistical analysis (mapping ratio, rRNA/mtRNA content, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤ 20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software.
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM (fragments per kilobase of transcript per million mapped reads) in group ≥ 0.5. FPKM is equal to the number of fragments that map a certain gene or transcipt times a million divided by the length of the gene in Kb and the fragmnets number that map to all genes/transcripts.
Differentially expressed gene and transcript analyses were performed with R package ballgown. Fold change (cutoff 1.5), p-value (≤ 0.05) and FPKM (≥ 0.5 mean in one group) were used for filtering differentially expressed genes and transcripts.
Genome_build: CanFam3
Supplementary_files_format_and_content: Expression_Gene.xlsx file contains in column A the Track_id which is the database name in gene level, in column B the name of the gene, in column C its locus, in column D the strand of the gene, in column E the gene type and in colunms F through U the FPKM of each gene for each one of the samples. Likewise, Expression_Transcript.xlsx file contains in column A the Track_id which is the database name in transcript level, in column B the name of the transcript, in column C the ENSEMBL gene id of the transcript, in column D the name of the gene, in column E the locus, in column F the strand, in column F the biological type of the transcript and in colunms H through W the FPKM of trasncript in samples. Differentially_Expressed_Genes.xlsx and Differentially_Expressed_Transcripts.xlsx show differentially expressed genes or transcripts when comparisons between different groups os samples are performed. Different groups compared are shown in different sheets within the xlsx file.

organism: Canis lupus familiaris

growth_protocol:
In DMEM media supplemented with fetal bovine serum to a final concentration of 10%
G-MDCK cells were cultured in high glucose DMEM medium (Thermofisher; 11965092) containing 4500 mg/L glucose and supplemented with 10% FBS (GemBio; 900-108) as previously suggested. To generate confluent cell monolayers, 24-well plates glass-bottom for microscopy were coated with 50 µg/ml rat-tail collagen-I (diluted in 0.2 N acetic acid) for 1 h at 37°C, air-dried for 15 min, and UV-sterilized for 30 min in a tissue culture hood. MDCK cells were seeded at a density of 2 × 10^5 cells/well for 24 h.

extract_protocol:
Cells were harvested and lyzed using the QIAshredder Kit (Qiagen; 79656). mRNA was harvested using the RNeasy Plus Micro Kit (Qiagen; 74004) and eluted in 30 μL RNAase free water. RNA concentrations were measured using the nanodrop machine and were comparable between conditions. RNA quality and quantity were confirmed via bioanalyzer analysis performed by Arraystar Inc.
The total RNA was depleted of rRNAs by Arraystar rRNA Removal Kit. We used Illumina kits for the RNA-seq library preparation, which included procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Finally, the prepared RNA-seq libraries were qualified using Agilent 2100 Bioanalyzer and quantified by qPCR absolute quantification method
The DNA fragments in well mixed libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, loaded onto channels of the flow cell at 8 pM concentration, and amplified in situ using TruSeq SR Cluster Kit v3-cBot-HS (#GD-401-3001, Illumina). Sequencing was carried out using the Illumina X- ten/NovaSeq according to the manufacturer’s instructions. Sequencing was carried out by running 150 cycles.

treatment_protocol: 24 h post-seeding MDCK cells were exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria three times with PBS, media containing 20 μg/mL gentamycin was added to cells to kill extracellular bacteria. 24 h post-infection cells were trypsinized and either left in tubes or sorted to infected and uninfected populations. All tubes containing cells in solution were treated in parallel so to lyze the cells and extract their RNA.

value: Madin-Darby Canine Kidney (G-MDCK) epithelial cells

value: kidney tubule

tag: nature

value: immortalized

tag: vendor/source

value: Obtained from the Bakardjiev lab, UCSF (previously obtained from ATCC)


title: UID - sorted uninfected cells from infected well


title: 6hr_infected.E10.batch1

value: epithelial (HEp2)


title: 3BMB_80


title: 3BMB_119


title: 6hr_infected.F10.batch1


title: UIB - sorted uninfected cells from infected well


title: UIA - sorted uninfected cells from infected well


title: 3BMB_172


title: 6hr_infected.D9.batch1


title: 6hr_infected.D10.batch1


title: 3BMB_133


title: IID - sorted infected cells from infected well

description: 2x10^5 cells grown on 12 mm collagen I coated glass coverslips for 24 h were then exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria, media containing 20 μg/mL gentamycin was added to cells. 24 h post-infection cells were trypsinized, uninfected cells were  flow sorted and then RNA was extracted.


title: 3BMB_21


title: 6hr_infected.C9.batch1


title: 3BMB_161


title: 3BMB_1


title: 3BMB_24


title: 3BMB_138


title: 3BMB_85


title: 3BMB_142


title: 3BMB_6


title: 3BMB_22


title: IIB - sorted infected cells from infected well


title: 3BMB_52


title: 3BMB_25


title: 3BMB_105


title: IIC - sorted infected cells from infected well


title: 6hr_infected.C10.batch1


title: 3BMB_174


title: 3BMB_41


title: 3BMB_7


title: 6hr_infected.B9.batch1


title: IIA - sorted infected cells from infected well


title: 6hr_infected.B10.batch1


title: 3BMB_84


title: 3BMB_128


title: AID - all cells from infected well

description: 2x10^5 cells grown on 12 mm collagen I coated glass coverslips for 24 h were then exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria, media containing 20 μg/mL gentamycin was added to cells. 24 h post-infection cells where trypsinized and RNA was extraceted from all cells in the infected well.

source_name: all cells from infected well


title: 6hr_infected.A9.batch1


title: AIC - all cells from infected well


title: 3hr_mock_infected.H6.batch3


title: 6hr_infected.A10.batch1


title: AIB - all cells from infected well


title: AIA - all cells from infected well


title: 3hr_mock_infected.H5.batch3


title: 3hr_mock_infected.G5.batch3


title: 3hr_mock_infected.F6.batch3


title: 3BMB_70


title: 3BMB_61


title: 3hr_mock_infected.F5.batch3


title: 3BMB_17


title: 3BMB_243


title: 3BMB_158


title: Samp_85774_Incubating_VmT

city: Bloomington

first: Kimberly

last: Rosvall

state: IN

address: 1001 E Third Street

institute: Indiana University

description:
VmT_INC_85774
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic (version 0.36) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17
Reads were mapped to the transcriptome using Bowtie2 (version 2.3.4.1).
Reads mapped to transcripts were counted using Samtools (version 1.3.1 ) and custom perl scripts.
R (version 3.4.1) and DESeq2 (version 1.16.1) were used to perform differential expression analysis.
Genome_build: transcripts.mrna_pub.fa (GEO Accession GSE126210)
Supplementary_files_format_and_content: GSF1579_FPKM_geneMatrix_NORMALIZED.csv: Comma-delimited FPKM values

organism: Tachycineta bicolor

source_name: Sample 85774 Incubating Ventromedial Telencephalon

extract_protocol:
Tissues were removed, flash frozen on dry ice, and total RNA was extracted using Trizol reagent. TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; however, when preparing larger fragments, the fragmentation step was reduced from 8min to 10s at 94oC.

value: Ventromedial Telencephalon

tag: breeding stage

value: Incubating

tag: Sex

value: Female

tag: individual


title: Samp_85840_Incubating_VmT

description:
VmT_INC_85840
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85840 Incubating Ventromedial Telencephalon

tag: tissue


title: Samp_85889_Incubating_VmT

description:
VmT_INC_85889
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85889 Incubating Ventromedial Telencephalon


title: Samp_85899_Incubating_VmT

description:
VmT_INC_85899
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85899 Incubating Ventromedial Telencephalon


title: 3BMB_78

value: lung


title: 3BMB_123


title: Samp_85757_Incubating_VmT

description:
VmT_INC_85757
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85757 Incubating Ventromedial Telencephalon


title: 3BMB_113


title: 3BMB_93


title: 3BMB_8


title: 3BMB_57


title: 3BMB_35


title: 3BMB_56


title: 3BMB_159


title: 3BMB_154


title: 3BMB_79


title: 3BMB_96


title: 3BMB_102


title: 3hr_mock_infected.E5.batch3

source_name: Epithelial cells (HEp2)

value: mock infected


title: Samp_85694_Early_VmT

description:
VmT_TE_85694
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85694 Early Ventromedial Telencephalon

value: Early


title: 3hr_mock_infected.E6.batch3


title: Samp_85692_Early_VmT

description:
VmT_TE_85691
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85692 Early Ventromedial Telencephalon


title: Samp_85691_Early_VmT

description: processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85691 Early Ventromedial Telencephalon


title: 3hr_mock_infected.D5.batch3


title: 3BMB_59


title: 3BMB_110


title: 3BMB_162


title: 3BMB_145


title: 3hr_mock_infected.C5.batch3


title: Samp_85674_Early_VmT

description:
VmT_TE_85674
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85674 Early Ventromedial Telencephalon


title: 3hr_mock_infected.B6.batch3


title: Samp_85899_Incubating_HYPO

description:
HYPO_INC_85899
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85899 Incubating Hypothalamus

value: Hypothalamus


title: 3hr_mock_infected.B5.batch3


title: 3hr_mock_infected.D6.batch3


title: 3hr_mock_infected.A6.batch3


title: Samp_85689_Early_VmT

description:
VmT_TE_85689
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85689 Early Ventromedial Telencephalon


title: Samp_85889_Incubating_HYPO

description:
HYPO_INC_85889
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85889 Incubating Hypothalamus


title: 3hr_mock_infected.C6.batch3


title: Samp_85840_Incubating_HYPO

description:
HYPO_INC_85840
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85840 Incubating Hypothalamus


title: 3BMB_20


title: 3BMB_58


title: 3BMB_126


title: 3BMB_40


title: 3BMB_89


title: 3BMB_176


title: 3BMB_43


title: 3BMB_167


title: 3BMB_104


title: Samp_85774_Incubating_HYPO

description:
HYPO_INC_85774
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85774 Incubating Hypothalamus


title: 3BMB_179

source_name: lung biopsy


title: 3BMB_87


title: 3BMB_13


title: Samp_85757_Incubating_HYPO

description:
HYPO_INC_85757
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85757 Incubating Hypothalamus


title: 3hr_mock_infected.A5.batch3


title: 3BMB_3


title: 3BMB_55


title: 3hr_mock_infected.H4.batch2


title: Samp_85694_Early_HYPO

description:
HYPO_TE_85694
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85694 Early Hypothalamus


title: 3hr_mock_infected.H3.batch2


title: 3BMB_242


title: 3hr_mock_infected.G4.batch2


title: Samp_85692_Early_HYPO

source_name: Sample 85692 Early Hypothalamus


title: Samp_85691_Early_HYPO

description:
HYPO_TE_85691
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85691 Early Hypothalamus


title: 3BMB_71


title: 3BMB_139


title: 3hr_mock_infected.A1.batch3


title: 3BMB_92


title: 3hr_mock_infected.G3.batch2


title: 3hr_mock_infected.F4.batch2


title: 3BMB_107


title: 3BMB_34


title: Samp_85674_Early_HYPO

description:
HYPO_TE_85674
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85674 Early Hypothalamus


title: 3hr_mock_infected.F3.batch2


title: Samp_85689_Early_HYPO

description:
HYPO_TE_85689
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85689 Early Hypothalamus


title: Samp_85899_Incubating_HB

description:
HB_INC_85899
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85899 Incubating Hindbrain

value: Hindbrain


title: 3BMB_95


title: 3BMB_31


title: Samp_85889_Incubating_HB

description:
HB_INC_85889
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85889 Incubating Hindbrain


title: Samp_85840_Incubating_HB

description:
HB_INC_85840
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85840 Incubating Hindbrain


title: 3hr_mock_infected.E4.batch2

source_name: Epithelial cells (HEp2)


title: 3hr_mock_infected.E3.batch2


title: 3BMB_48


title: Samp_85774_Incubating_HB

description:
HB_INC_85774
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85774 Incubating Hindbrain


title: 3BMB_74


title: 3BMB_47


title: 3hr_mock_infected.D4.batch2


title: 3BMB_155


title: 3BMB_9


title: 3BMB_42


title: 3hr_mock_infected.D3.batch2


title: 3hr_mock_infected.C4.batch2


title: 3BMB_60


title: Samp_85757_Incubating_HB

description:
HB_INC_85757
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85757 Incubating Hindbrain


title: 3BMB_115


title: 3BMB_117


title: Samp_85694_Early_HB

description:
HB_TE_85694
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85694 Early Hindbrain


title: 3BMB_64


title: 3BMB_175


title: 3BMB_101


title: 3BMB_37


title: 3BMB_62


title: 3BMB_183


title: 3hr_mock_infected.C3.batch2


title: 3BMB_118


title: 3BMB_75


title: 3BMB_178


title: 3BMB_68


title: Samp_85692_Early_HB

description: processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85692 Early Hindbrain


title: 3hr_mock_infected.B4.batch2


title: 3hr_mock_infected.B3.batch2


title: Samp_85689_Early_HB

description:
HB_TE_85689
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85689 Early Hindbrain


title: 3BMB_81


title: 3hr_mock_infected.A4.batch2


title: Samp_85691_Early_HB

description:
HB_TE_85691
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85691 Early Hindbrain


title: TRES_muscle_NextSeq

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic (version 0.36) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17
MiSeq and NextSeq reads were assembled with Spades (v3.11.1) with 3 different parameter sets: -k 35, -k 55, -k 127
MiSeq and NextSeq reads were assembled with Trinity (v2.6.5)
EviGene (by Don Gilbert) was used to combine assemblies and determine the final transcriptome
Reads were mapped to the transcriptome using STAR (version 2.5.2a) with following optional parameters: --outFilterMultimapNmax 1 --seedSearchStartLmax 16 --quantMode GeneCounts --twopassMode Basic  --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3
Genome_build: transcripts.mrna_pub.fa
Supplementary_files_format_and_content: Tab-delimited gene counts mapped to transcriptome

source_name: female tree swallows_pectoral muscle

value: female

tag: developmental stage

value: adult

value: pectoral muscle


title: 3hr_mock_infected.A3.batch2


title: 3BMB_66

source_name: lung biopsy


title: Samp_85674_Early_HB

description:
HB_TE_85674
processed data file: GSF1579_FPKM_geneMatrix_NORMALIZED.csv

source_name: Sample 85674 Early Hindbrain


title: 3hr_infected.H7.batch3

value: infected

value: Chlamydia trachomatis - Serovar E


title: TRES_liver_NextSeq

source_name: female tree swallows_liver

value: liver


title: 3BMB_76


title: 3BMB_239


title: 3BMB_12


title: 3BMB_240


title: 3BMB_237


title: 3hr_infected.G7.batch3


title: 3hr_infected.H6.batch3


title: TRES_brain_NextSeq

source_name: female tree swallows_brain

value: brain


title: 3BMB_236


title: 3BMB_238


title: 3BMB_241


title: 3BMB_46


title: TRES_spleen_NextSeq

source_name: female tree swallows_spleen

value: spleen


title: 3BMB_234


title: 3hr_infected.G6.batch3

value: epithelial (HEp2)


title: 3BMB_146


title: TRES_ovary_NextSeq

source_name: female tree swallows_ovary

value: ovary


title: 3hr_infected.F7.batch3


title: TRES_blood_NextSeq

source_name: female tree swallows_trunk blood

value: trunk blood


title: 3BMB_232


title: 3hr_infected.E7.batch3


title: 3BMB_231


title: 3BMB_235


title: 3BMB_229


title: 3hr_infected.D7.batch3


title: 3BMB_230


title: 3hr_infected.E6.batch3


title: 3hr_infected.D6.batch3


title: 3hr_infected.C7.batch3


title: 3BMB_226


title: 3BMB_228


title: 3BMB_224


title: 3hr_infected.F6.batch3


title: 3BMB_219


title: 3BMB_220


title: TRES_muscle_MiSeq


title: 3BMB_233


title: TRES_spleen_MiSeq


title: 3BMB_227


title: 3BMB_221


title: 3BMB_223


title: 96729

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
We used our in-house analysis pipeline to perform adapter trimming, quality control, and processing for the RNA-seq samples.
Reads were mapped to the reference genome (NCBI build 37) using STAR
Gene expression levels were measured by HTSeq using GENCODE v24 as the gene annotation database
Only genes with more than 1 read/sample on average were retained for analysis.
Genome_build: NCBI build 37
Supplementary_files_format_and_content: genes x samples raw count matrix

source_name: PBMC

extract_protocol:
Substrate-attached cells were dislodged by pipetting and combined with floating cells, and total RNA was isolated using a RNeasy plus mini kit (Qiagen, Germantown, MD).
Sequencing libraries were prepared from the RNA using the Takara SMARTer pico input mammalian stranded total RNA sequencing kit (Takara Bio USA, San Francisco, CA).
The libraries were sequenced on an Illumina NextSeq instrument using 75 cycles to obtain a normalized read depth of 15-20 million reads per sample

treatment_protocol: PBMCs were cultured for 7 days with CD3/CD28 Dynabeads in the presence or absence of spontaneous NETs or NETs formed with exposure to 5 ng/ml LPS.

tag: patientid

tag: traf3ip2 genotype


title: TRES_liver_MiSeq


title: TRES_brain_MiSeq


title: 3BMB_222


title: 3BMB_213


title: 3BMB_216


title: 3BMB_215


title: 3hr_infected.A7.batch3

tag: condition


title: 3BMB_210


title: TRES_blood_MiSeq


title: 3hr_infected.A6.batch3


title: 3BMB_225


title: 3BMB_208


title: 3hr_infected.C6.batch3


title: 3hr_infected.B7.batch3


title: 3BMB_217


title: 3BMB_207


title: 3BMB_205


title: 3hr_infected.H5.batch2


title: 3hr_infected.H4.batch2


title: 96725


title: 3hr_infected.B6.batch3


title: 96724


title: 3BMB_209


title: 3BMB_218


title: 96727


title: 3BMB_212


title: 96730


title: 3BMB_211


title: 96723


title: 3BMB_204


title: 96726


title: 3BMB_214


title: TRES_ovary_MiSeq


title: 3BMB_206


title: 96721


title: 3hr_infected.F4.batch2


title: 3hr_infected.G5.batch2


title: 96720


title: 3hr_infected.G4.batch2


title: 3hr_infected.F5.batch2


title: 96719


title: 3BMB_202


title: 3BMB_203


title: 3BMB_173


title: 3hr_infected.E5.batch2


title: 3BMB_73


title: 3BMB_182


title: 3BMB_201


title: 96722


title: 3BMB_200


title: 3BMB_121


title: 3hr_infected.E4.batch2


title: 3hr_infected.D5.batch2


title: 96717


title: 3hr_infected.D4.batch2


title: 3BMB_164


title: 3hr_infected.C5.batch2


title: 96718


title: 96716


title: 3BMB_196


title: 3BMB_114


title: 96714

value: wt


title: 3hr_infected.C4.batch2


title: 3BMB_199

value: lung


title: 3hr_infected.B5.batch2


title: 3BMB_198


title: 3BMB_195


title: 96715


title: 96712


title: 3hr_infected.B4.batch2


title: 96713


title: 3BMB_193


title: 3hr_infected.A5.batch2


title: 96711


title: 3BMB_197


title: 3hr_infected.A4.batch2


title: IRF4 MKO1284

city: LOS ANGELES

first: Xingxing

last: Kong

address: UCLA PEDIATRICS, 10833 LE CONTE AVE, CHS-MARION DAVIES CHILDREN CTR

institute: UCLA

data_processing:
The data was sequenced on HiSeq3000 to generate single-read 50bp reads. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M-values) was used to normalize the gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Text files include RSEM values for each Sample.

source_name: Skeletal muscle (Soleus)

extract_protocol:
Skeletal muscle was removed, flash frozen on liquid nitrogen, and RNA was harvested using RNA Sample Prep Kit.
Libraries for RNA-Seq were prepared with Kapa Stranded mRNA. The workflow consisted of mRNA enrichment, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification.

tag: strain

value: Male

tag: food

value: High fat diet


title: 3BMB_116


title: 96710


title: IRF4 MKO1283


title: 3BMB_109


title: 3BMB_120


title: 3BMB_2


title: 3BMB_94


title: 3BMB_63


title: 3BMB_191


title: 3BMB_169


title: 3BMB_124


title: 3hr_infected.H11.batch1

source_name: Epithelial cells (HEp2)


title: IRF4 MKO1223


title: 96709


title: 3hr_infected.H10.batch1


title: IRF4 MKO1221


title: 96707


title: 3BMB_192


title: Flox1285


title: 3BMB_190


title: 3hr_infected.G10.batch1


title: 3hr_infected.G11.batch1


title: 3BMB_103


title: 3BMB_82


title: Flox1282


title: 96708


title: 3BMB_32


title: 96706


title: Flox1224


title: 96705


title: 96704


title: 3hr_infected.E11.batch1


title: 96702


title: 96701


title: 96700


title: 3hr_infected.F11.batch1


title: 3hr_infected.D11.batch1


title: 3BMB_170


title: 3BMB_15


title: 3hr_infected.F10.batch1


title: Flox1281


title: 3hr_infected.D10.batch1


title: 96699


title: 3BMB_134


title: 5_AI_30

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

description: Chronic bladder ischemia_#3

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools(APT). We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis.
Statistical significance of the expression data was determined using independent t-test and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm. For a DEG set, Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity.
Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using Gene Ontology (http://geneontology.org) and KEGG(http://kegg.jp).
All data analysis and visualization of differentially expressed genes was conducted using R 3.0.2 (www.r-project.org).

organism: Rattus norvegicus

source_name: Bladder

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Male 16-weeks old Sprague–Dawley rats were subjected to arterial injury (AI) with 30 times (AI-30). The AI-30 inury was carried out to induce endothelial injury of the bilateral iliac arteries using the 2-French forgartic catheter. The sham group underwent sham operation.

extract_protocol: Total RNA from the indicated bladder tissues was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN)

treatment_protocol: Animals in sham and AI-30 groups received a 2% cholesterol diet. After 8 weeks, all rats were sacrfied and whole bladder tissues were prepared to isolate total RNA.

value: Sprague-Dawley

tag: gender

value: male

tag: group

value: iliac arterial injury

value: Bladder

tag: age

value: 24 weeks


title: 3BMB_184


title: 3hr_infected.E10.batch1

data_processing:
Base calls were performed using the bulit in Illumina basecaller and demultiplexed using DeML
Sequenced reads were trimmed and quality checked using Trim Galore (v.0.4.3), FastQC (v.0.11.5) and FastQ-Screen (v.0.11.1)
Trimmed reads were aligned to the human genome (GRCh 38.87) using STAR (v.2.5.1a) keeping paired and unpaired aligned reads, genomic features were counted with FeatureCounts (v.1.5.0-p3)
Genome_build: Genome Reference Consortium Human Build 38 patch release 87 (GRCh38.p87)
Supplementary_files_format_and_content: Count matricies generated from each of the raw BAM files using FeatureCounts

value: infected

tag: hours post infection

tag: sequencing batch

tag: chlamydial species


title: 4_AI_30

description: Chronic bladder ischemia_#2


title: 1_AI_30

description: Chronic bladder ischemia_#1


title: 3BMB_97


title: 3BMB_194


title: 3hr_infected.C10.batch1

tag: cell type

value: Chlamydia trachomatis - Serovar E


title: 96698


title: 96697


title: 3hr_infected.B11.batch1


title: 96696


title: 3hr_infected.B10.batch1


title: 3hr_infected.C11.batch1


title: 96695


title: 96694


title: 3hr_infected.A11.batch1


title: 96693


title: 3hr_infected.A10.batch1


title: 96728


title: 5_sham

description: control replicate#3

value: sham


title: 3BMB_165


title: TGFb1_Cells_3

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

data_processing:
Fastq files were obtained from BGI
Gene quantification (read count and normalised expression value as FPKM) was obtained using RSEM 1.3.0 (options: -bowtie2 -forward-prob 0 -paired-end), based on GENCODE annotation version 25 (primary assembly).
Adapter and low quality sequences were removed using TrimGalore. Mapping was done using STAR based on GENCODE primary assembly GRCh38 genome and transcriptome version 26. Gene quantification was done using HTseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file with raw read count obtained by HTseq-count

source_name: HPASMC

growth_protocol: Cultures of HPASMCs have been described previously (Deng et al, 2015. Circulation research). The culture was done using FBS depleted of EVs by overnight ultracentrifugation at 100,000·g.

extract_protocol:
RNA from HPASMCs and EVs was extracted with miRNeasy kit (Qiagen), quantified using Qubit technology and quality checked with the Agilent Bioanalyzer. The total amount of RNA obtained from EVs was 9 ng, thus we utilised a low-input RNA-Seq approach.
Library preparation was done with SMARTer Low-Input Strand-Specific Total RNASeq for Illumina and sequenced on a HiSeq 4000 by BGI Tech

treatment_protocol: Stimulation of HPASMCs was performed with TGF-β1 (10 ng/ml) or BMP4 (10 ng/ml) for 48h renewing stimuli every 24 h. For the Isolation of EVs, supernatants were centrifuged at 2000·g for 10’ at 4°C to remove dead cells. Then EVs were isolated by means of two steps of ultracentrifugation at 100,000·g for 1h at 4°C. The EV population in this pellet was confirmed by Nano Tracking Analysis (NTA) and western blot analysis for CD63 (EV marker) and His3 (nuclear marker, negative control).

value: HPASMC

tag: treatment

tag: rna source (evs/cells)

value: Cells

tag: replicate

value: replicate 3


title: F1 leaf 2 rep2

city: West Lafayette

first: Meixia

last: Zhao

address: 915 W State Steet

department: Agronomy

institute: Purdue University

description: total small RNA

data_processing:
Base-calling
The small RNA sequencing data from different libraries was trimmed and filtered for low quality reads, adapter sequences, and reads matching structural noncoding RNAs (t/r/sn/snoRNAs) collected from Rfam (http://rfam.sanger.ac.uk). The kept reads with a length of 18-26 nt were mapped to MuDR(p1) and Muk, and their flanking 500 bp upstream and downstream sequences using Bowtie only allowing perfect matches.
Small RNA abundance was normalized to reads per million.
The data was viewed using Intergrative Genomics Viewer. Small RNAs for the mop1 and lbl1 mutants were downloaded from previous studies, trimmed and mapped to MuDR sequences.
Genome_build: MuDR (M76978.1) and Muk (DQ011286.1)
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

organism: Zea mays

source_name: Leaf 2

growth_protocol: greenhouse with a 12 hour light cycle

extract_protocol:
Total RNA was extracted using an SDS-based extraction solution and precipitated using ethanol. The pellet was dissolved in water, heated to 65°C for 5 min, and then placed on ice. Polyethylene glycol (molecular weight 8000; Sigma) was added to a final concentration of 5% and NaCl to a final concentration of 0.5 M. After an 1 hour incubation on ice, the RNA was centrifuged at 10,000g for 10 min. Three volumes of ethanol were added to the supernatant, and the RNA was precipitated at –20°C for at least 2 hrs. The low molecular weight RNAs were pelleted by centrifugation for 10 min at 10,000g. Small RNAs were detected in Polyacrylamide gel electrophoresis (PAGE) gel and purified by ZR small-RNA™ PAGE Recovery Kit.
Small RNA library was prepared by ScriptMiner™ Small RNA-Seq Library Preparation Kit for Ilumina sequencing.

tag: tissue

value: Leaf

tag: genotype

tag: Stage

value: Young leaf 2


title: no MuDR no Muk rep2

description: total small RNA

value: tester control (IT)


title: 3BMB_135

value: lung


title: Muk only rep2

description: total small RNA

value: Muk (Muk/-)


title: MuDR only rep2

description: total small RNA

value: MuDR (p1/-)


title: F1 leaf 6 rep2

description: total small RNA

source_name: Leaf 6

value: Young leaf 6


title: TGFb1_Cells_2

value: replicate 2


title: 3BMB_163


title: 3BMB_4


title: 3BMB_51


title: 3BMB_14


title: 3BMB_98


title: 3BMB_29


title: 96691

tag: patientid

tag: traf3ip2 genotype


title: 3_sham

description: control replicate#1

tag: strain

value: Sprague-Dawley

value: male


title: 3BMB_171


title: F1 leaf 6 rep1

description: total small RNA


title: 3BMB_19


title: 4_sham

description: control replicate#2

value: Bladder

value: 24 weeks


title: TGFb1_Cells_1

value: replicate 1


title: 96692

tag: condition


title: 3BMB_127


title: 96690


title: 96688


title: Muk only rep1

description: total small RNA


title: 96687


title: MuDR only rep1

description: total small RNA


title: BMP4_Cells_2


title: 96686


title: no MuDR no Muk rep1

description: total small RNA


title: BMP4_Cells_3


title: 3BMB_83


title: BMP4_Cells_1


title: Untreated_Cells_3

value: Untreated


title: 96684


title: 96685


title: Untreated_Cells_2

value: HPASMC


title: F1 leaf 2 rep1

description: total small RNA


title: TGFb1_EV_3

value: EVs


title: 96683


title: 96682


title: TGFb1_EV_2


title: 96681


title: 3BMB_23


title: 3BMB_150


title: 3BMB_129


title: 3BMB_67


title: BMP4_EV_3

value: replicate 3


title: 3BMB_151


title: 96680